Description of problem:
By default X comes up with 1280x1600 resolution, and after appearing to
successfully change to 1024x768 via system-configure-display followed by logging
out and back in again, the updated resolution didn't appear. I was able to work
around this by hand-editing xorg.conf, but I wonder why the same couldn't be
accomplished via the GUI.
I noticed a very similar bug reported against FC4 at
https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=176592

FC6 with all updates as of 12/2/06 allows root user to set screen resolution.
This setting does not affect the screen resolution of other users. If logged in
as a user other than root, setting the display resolution requires the temporary
root password, and allows the setting, but after logging out and back in, the
resolution has reverted.